akre96/nextflow_test

Example NextFlow Workflow to Read Database

This is intended as an example script for how to use nextflow to run analyses using the HPC

Steps

1. Log in to the HPC environment
2. Start a tmux session
   • tmux new -s nextflow_test
3. Enter an interactive node
   • srun --exclusive --partition F2 --pty bash
4. Download nextflow if not already installed
   • curl -s https://get.nextflow.io | bash
   • creates nextflow in home directory, may need to chmod to allow execution
5. Clone this repository
   • git clone https://github.com/akre96/nextflow_test.git
6. Enter the repository: cd nextflow_test
7. Run the nextflow query
   • ../nextflow run query_db.nf --study [study_name]
   • Example: ../nextflow run query_db.nf --study pilot